We study theoretically quantum states of a pair of photons interacting with a finite periodic array of two-level atoms in a waveguide. Our calculation reveals two-polariton eigenstates that have a highly irregular wave function in real space. This indicates the Bethe ansatz breakdown and the onset of quantum chaos, in stark contrast to the conventional integrable problem of two interacting bosons in a box. We identify the long-range waveguide-mediated coupling between the atoms as the key ingredient of chaos and nonintegrability. Our results provide new insights in the interplay between order, chaos, and localization in many-body quantum systems and can be tested in state-of-the-art setups of waveguide quantum electrodynamics.